Wearing a dark suit and sweating before the cameras, Mali's prime minister, Cheikh Modibo Diarra, announced his resignation on Tuesday in a live 4am broadcast on state television, admitting: "Our country is living through a period of crisis."

The 60-year-old former astrophysicist, who worked for Nasa and Microsoft, had been arrested hours earlier and forced to quit by the country's military junta.

France called for a new government to be formed quickly and said the turn of events enhanced the case for foreign military intervention. But observers warned that plans for a UN-backed force to combat Islamist insurgents in northern Mali were now "on ice".

Diarra was preparing to leave for France when soldiers reportedly smashed down the door of his home, bundled him into a car and drove to the Kati military camp, a sprawling base where a coup was launched on 21 March.

Hours later, a bare wall behind him, he addressed the nation (video) with an apology. "Our country is living through a period of crisis," he said. "Men and women who are worried about the future of our nation are hoping for peace. It's for this reason that I, Cheikh Modibo Diarra, am resigning along with my entire government on this day, Tuesday, 11 December 2012. I apologise before the entire population of Mali."

For several weeks tension has been mounting between the officers who led the coup and Diarra, the civilian prime minister whom they were forced to appoint when they handed power back to a transitional government. Bakary Mariko, a spokesman for the junta, said Diarra was forced out because he was "not getting along" with the interim president or coup leader captain Amadou Haya Sanogo.

"It's the reason why Mali's army has taken things into their own hands and told Cheikh Modibo Diarra to resign for the good of Mali," Mariko told the Associated Press.

He added: "For several days now, Cheikh Modibo Diarra has mobilised his supporters and boycotted the national conference [currently being held to discuss Mali's future]. And now he says he's going to Paris for medical tests … but we know better and realise that he is trying to flee in order to go and create a blockage in the Mali situation."

In a separate interview with Reuters, Mariko said: "The country is in crisis but he was blocking the institutions. This is not a coup. The president is still in place but the prime minister was no longer working in the interests of the country."

A foreign diplomat, who did not wish to be named, said Diarra's claim that he was going to Paris for medical tests rang true. "Enough people have told me he was genuinely ill."

Diarra remained under house arrest and military guard on Tuesday. The Mali capital, Bamako, appeared calm but the humiliating exit illustrated how the junta still calls the shots, even though the soldiers made a show in April of handing power back to civilians.

Last weekend Diarra helped organise a demonstration calling for a UN-backed military intervention in north Mali, which fell to Islamist militants in the wake of the coup and provides a haven for al-Qaida affiliates. On Monday, EU foreign ministers approved training for a mission involving Malian and other African troops.

In response to Diarra's resignation, Philippe Lalliot, a French foreign ministry spokesman, said: "These developments underline the need for the rapid deployment of an African stabilisation force."

But the Bamako-based diplomat warned: "All the things we've talked about are on ice, at least. Everyone's waiting to see what happens next."

That view was echoed by the German foreign minister, Guido Westerwelle. "One thing is clear: our offers of help come with the condition that the process of restoring constitutional order in Mali be conducted credibly. And it is only that way that the crisis in northern Mali can be resolved.

"Interim president [Dioncounda] Traoré and all the country's political leaders must now act responsibly so that Mali returns to stability," he said.

But there are doubts over whether Traoré can assert his authority. In May Yerewoloton, a violent citizens' movement believed to be backed by the junta, broke through the security cordon at the presidential palace and severely beat the 70-year-old.

A police officer who was on duty Monday night at Bamako's international airport said the same group stormed the airport before the prime minister was to fly to Paris.

"The plane that was to take the prime minister to France was on the point of departure," he told AP. "It was stopped by people from the group Yerewoloton who invaded the airport. The people from Yerewoloton are still at the airport as we speak, searching cars."

The developments did not surprise analysts such as Gilles Yabi, west Africa project director of the International Crisis Group. "There was clearly a lot of tension between the prime minister and the junta," he said. "It was difficult to believe it could work for a long period; the situation wasn't stable and anything could happen."

A concerted effort to reclaim the north seems a distant prospect. "Even before this we were still very far from seeing a resolution in the north," Yabi added. "This is delaying the process again. If we don't have a real government in Bamako with a vision for the nation, you can't expect the international community to make the commitment."

Human Rights Watch's senior researcher for west Africa, Corinne Dufka, condemned the military's intervention, saying it fits with the pattern of abuse by the soldiers ever since the coup eight months ago.

"They've arrested, beaten and intimidated journalists; tortured and disappeared military rivals; and now, apparently, arbitrarily detained the prime minister. None of these incidents have been investigated and those responsible appear to have been emboldened by the shameful lack of accountability."

The US warned on Monday that Mali is "one of the potentially most explosive corners of the world".